Re: [MORPHMET] A question about PCA in geomorph
Dear Emma ALL, Indeed, when reading my data with readland.nts I get the data in the format required by the geomorph analytical routines. The problem is that I was calling by mistake a routine from Ian Dryden's shapes package (procGPA) to generate the Procrustes-aligned coordinates, instead of the gpagen routine. Fixed this and now everything works fine. I take this opportunity to ask another question, this time relating to the plots generated by geomorph. Is there a way to customize them, including for example axis labels in the PCA plots? In fact, the Quick Guide shows these plots with labels, but I could not figure out how to include them in my plots. Calling the R par function (as one should have done when using the usual plot command) did not work. Again, thanks for your help. Best regards,. 2015-04-12 1:39 GMT-03:00 Emma Sherratt emma.sherr...@gmail.com: Mauro, If you read in your NTS data file using readland.nts, it will automatically be in the 3D array format required by plotTangentSpace (after you use gpagen to do a Procrustes Superimposition). If you have your data as a 2D matrix, you simply use arrayspecs to make it a 3D array. Emma On Sunday, April 12, 2015, Mauro Cavalcanti mauro...@gmail.com wrote: Dear ALL, I have a number of questions about the geomorph R package, that I will post here in separate messages. First one concerns Principal Components Analysis, using the plotTangentSpace routine. It requires a 3D matrix as argument, however my data (on fishes) are 2D and I could not figure out how to convert my data to the required format; the explanation of the arrayspecs routine in the Quick Guide to Geomorph was not clear for me (and it lacks a workin exemple). My data are read from a NTSYSpc file containing 2D coordinates for 10 landmarks for a number of fish specimens, using the readland.nts routine. I have been able to perform a PCA on these data using the shapepca routine in Ian Dryden's shapes R package, but would like to perfom the entire analysis using geomorph. Thanks in advance for any hints! Best regards, -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: maurobio http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Twitter: @DrEmSherratt Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] A question about PCA in geomorph
Mauro, plus others, As a follow up, we are also working on a new function in geomorph to allow users to modify transformation (deformation) grids. Much like the R par function, this function will allow users to vary the colors, width, and style of grid lines and link links, the density of grid points, and the color and size of landmarks. This function will be available in the near future. Michael Collyer Assistant Professor Department of Biology Western Kentucky University 1906 College Heights Blvd. #11080 Bowling Green, KY 42101-1080 Phone: 270-745-8765; Fax: 270-745-6856 Email: michael.coll...@wku.edumailto:michael.coll...@wku.edu On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti mauro...@gmail.commailto:mauro...@gmail.com wrote: Dear Emma ALL, Indeed, when reading my data with readland.nts I get the data in the format required by the geomorph analytical routines. The problem is that I was calling by mistake a routine from Ian Dryden's shapes package (procGPA) to generate the Procrustes-aligned coordinates, instead of the gpagen routine. Fixed this and now everything works fine. I take this opportunity to ask another question, this time relating to the plots generated by geomorph. Is there a way to customize them, including for example axis labels in the PCA plots? In fact, the Quick Guide shows these plots with labels, but I could not figure out how to include them in my plots. Calling the R par function (as one should have done when using the usual plot command) did not work. Again, thanks for your help. Best regards,. 2015-04-12 1:39 GMT-03:00 Emma Sherratt emma.sherr...@gmail.commailto:emma.sherr...@gmail.com: Mauro, If you read in your NTS data file using readland.nts, it will automatically be in the 3D array format required by plotTangentSpace (after you use gpagen to do a Procrustes Superimposition). If you have your data as a 2D matrix, you simply use arrayspecs to make it a 3D array. Emma On Sunday, April 12, 2015, Mauro Cavalcanti mauro...@gmail.commailto:mauro...@gmail.com wrote: Dear ALL, I have a number of questions about the geomorph R package, that I will post here in separate messages. First one concerns Principal Components Analysis, using the plotTangentSpace routine. It requires a 3D matrix as argument, however my data (on fishes) are 2D and I could not figure out how to convert my data to the required format; the explanation of the arrayspecs routine in the Quick Guide to Geomorph was not clear for me (and it lacks a workin exemple). My data are read from a NTSYSpc file containing 2D coordinates for 10 landmarks for a number of fish specimens, using the readland.nts routine. I have been able to perform a PCA on these data using the shapepca routine in Ian Dryden's shapes R package, but would like to perfom the entire analysis using geomorph. Thanks in advance for any hints! Best regards, -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: maurobiohttp://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.orghttp://www.morphometrics.org/ To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.aumailto:emma.sherr...@une.edu.au Twitter: @DrEmSherratt Caecilians are legless amphibians... __ (\ .-. .-. /_) \\_/smb://_//^\\_//^\\_// `` `` `` learn more about them here: www.emmasherratt.com/caecilianshttp://www.emmasherratt.com/caecilians -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.commailto:mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.orghttp://www.morphometrics.org/ To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.orgmailto:morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] A question about PCA in geomorph
Michael, Thanks for your helpful message. Indeed, after posting my question about plot customization, I was able to generate a PCA plot from plotTangentSpace with axes labels, using the par function immediately before calling the plotTangentSpace routine, as follows: par(xlab=PC 1, ylab=PC 2). Obviously, the solution you suggested is even more generic and flexible and it also works fine. When means are available to customize the display of deformation grids, then geomorph will be near perfection! Thanks again for your help. With best regards, 2015-04-12 11:19 GMT-03:00 Collyer, Michael michael.coll...@wku.edu: Mauro, The extractable parts from prcomp() are also extractable from plotTangentSpace. One can make custom plots, relabel axes, change symbols, etc. Example: myplot = plotTangentSpace(mydata) attributes(myplot) # shows extractable parts PC.scores = myplot$x par(…) plot(PC.scores, …) Keep in mind with plotTangentSpace, the product is actually multiple plots, as the transformation grids are also plots. Therefore, it is not easy to pass on par() input to the result. But because users can extract the scores, all base R plotting functions are available. Cheers! -Mike Michael Collyer Assistant Professor Department of Biology Western Kentucky University 1906 College Heights Blvd. #11080 Bowling Green, KY 42101-1080 Phone: 270-745-8765; Fax: 270-745-6856 Email: michael.coll...@wku.edu On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti mauro...@gmail.com wrote: Dear Emma ALL, Indeed, when reading my data with readland.nts I get the data in the format required by the geomorph analytical routines. The problem is that I was calling by mistake a routine from Ian Dryden's shapes package (procGPA) to generate the Procrustes-aligned coordinates, instead of the gpagen routine. Fixed this and now everything works fine. I take this opportunity to ask another question, this time relating to the plots generated by geomorph. Is there a way to customize them, including for example axis labels in the PCA plots? In fact, the Quick Guide shows these plots with labels, but I could not figure out how to include them in my plots. Calling the R par function (as one should have done when using the usual plot command) did not work. Again, thanks for your help. Best regards,. 2015-04-12 1:39 GMT-03:00 Emma Sherratt emma.sherr...@gmail.com: Mauro, If you read in your NTS data file using readland.nts, it will automatically be in the 3D array format required by plotTangentSpace (after you use gpagen to do a Procrustes Superimposition). If you have your data as a 2D matrix, you simply use arrayspecs to make it a 3D array. Emma On Sunday, April 12, 2015, Mauro Cavalcanti mauro...@gmail.com wrote: Dear ALL, I have a number of questions about the geomorph R package, that I will post here in separate messages. First one concerns Principal Components Analysis, using the plotTangentSpace routine. It requires a 3D matrix as argument, however my data (on fishes) are 2D and I could not figure out how to convert my data to the required format; the explanation of the arrayspecs routine in the Quick Guide to Geomorph was not clear for me (and it lacks a workin exemple). My data are read from a NTSYSpc file containing 2D coordinates for 10 landmarks for a number of fish specimens, using the readland.nts routine. I have been able to perform a PCA on these data using the shapepca routine in Ian Dryden's shapes R package, but would like to perfom the entire analysis using geomorph. Thanks in advance for any hints! Best regards, -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: maurobio http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Twitter: @DrEmSherratt Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at
Re: [MORPHMET] A question about PCA in geomorph
Cheers Michael, I look forward to playing around with that! Tim *Tim Astrop PhD http://timastrop.wordpress.com/* Ammonoid Palaeobiology Lab http://aplbath.wordpress.com/ Department of Biology Biochemistry University of Bath On 12 April 2015 at 15:52, Collyer, Michael michael.coll...@wku.edu wrote: Mauro, plus others, As a follow up, we are also working on a new function in geomorph to allow users to modify transformation (deformation) grids. Much like the R par function, this function will allow users to vary the colors, width, and style of grid lines and link links, the density of grid points, and the color and size of landmarks. This function will be available in the near future. Michael Collyer Assistant Professor Department of Biology Western Kentucky University 1906 College Heights Blvd. #11080 Bowling Green, KY 42101-1080 Phone: 270-745-8765; Fax: 270-745-6856 Email: michael.coll...@wku.edu On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti mauro...@gmail.com wrote: Dear Emma ALL, Indeed, when reading my data with readland.nts I get the data in the format required by the geomorph analytical routines. The problem is that I was calling by mistake a routine from Ian Dryden's shapes package (procGPA) to generate the Procrustes-aligned coordinates, instead of the gpagen routine. Fixed this and now everything works fine. I take this opportunity to ask another question, this time relating to the plots generated by geomorph. Is there a way to customize them, including for example axis labels in the PCA plots? In fact, the Quick Guide shows these plots with labels, but I could not figure out how to include them in my plots. Calling the R par function (as one should have done when using the usual plot command) did not work. Again, thanks for your help. Best regards,. 2015-04-12 1:39 GMT-03:00 Emma Sherratt emma.sherr...@gmail.com: Mauro, If you read in your NTS data file using readland.nts, it will automatically be in the 3D array format required by plotTangentSpace (after you use gpagen to do a Procrustes Superimposition). If you have your data as a 2D matrix, you simply use arrayspecs to make it a 3D array. Emma On Sunday, April 12, 2015, Mauro Cavalcanti mauro...@gmail.com wrote: Dear ALL, I have a number of questions about the geomorph R package, that I will post here in separate messages. First one concerns Principal Components Analysis, using the plotTangentSpace routine. It requires a 3D matrix as argument, however my data (on fishes) are 2D and I could not figure out how to convert my data to the required format; the explanation of the arrayspecs routine in the Quick Guide to Geomorph was not clear for me (and it lacks a workin exemple). My data are read from a NTSYSpc file containing 2D coordinates for 10 landmarks for a number of fish specimens, using the readland.nts routine. I have been able to perform a PCA on these data using the shapepca routine in Ian Dryden's shapes R package, but would like to perfom the entire analysis using geomorph. Thanks in advance for any hints! Best regards, -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: maurobio http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Twitter: @DrEmSherratt Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
